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- PDB-9j61: Crystal structure of a cyclodipeptide synthase from Streptomyces ... -

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Basic information

Entry
Database: PDB / ID: 9j61
TitleCrystal structure of a cyclodipeptide synthase from Streptomyces sapporonensis
ComponentsCyclodipeptide synthase
KeywordsLIGASE / tRNA-Dependent enzyme / cyclodipeptide synthase
Function / homologyCyclodipeptide synthase / Cyclodipeptide synthase / Cyclodipeptide synthase superfamily / aminoacyltransferase activity / DI(HYDROXYETHYL)ETHER / Cyclodipeptide synthase
Function and homology information
Biological speciesStreptomyces cinnamoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, P. / Ren, Y. / He, J. / Wu, S. / Wang, J. / Tang, G. / Fang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Key Research and Development Program of China2022YFC2303100 China
CitationJournal: Biochemistry / Year: 2024
Title: Crystal Structure and Mutagenesis of an XYP Subfamily Cyclodipeptide Synthase Reveal Key Determinants of Enzyme Activity and Substrate Specificity.
Authors: He, J.B. / Ren, Y. / Li, P. / Liu, Y.P. / Pan, H.X. / Huang, L.J. / Wang, J. / Fang, P. / Tang, G.L.
History
DepositionAug 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclodipeptide synthase
B: Cyclodipeptide synthase
C: Cyclodipeptide synthase
D: Cyclodipeptide synthase
E: Cyclodipeptide synthase
F: Cyclodipeptide synthase
G: Cyclodipeptide synthase
H: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,78524
Polymers227,6878
Non-polymers1,09716
Water12,304683
1
A: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5232
Polymers28,4611
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7395
Polymers28,4611
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5232
Polymers28,4611
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7214
Polymers28,4611
Non-polymers2603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5232
Polymers28,4611
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5853
Polymers28,4611
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cyclodipeptide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7095
Polymers28,4611
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Cyclodipeptide synthase


Theoretical massNumber of molelcules
Total (without water)28,4611
Polymers28,4611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.590, 89.440, 93.350
Angle α, β, γ (deg.)70.850, 67.037, 61.542
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein
Cyclodipeptide synthase


Mass: 28460.918 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Gene: bcmA, BLA24_33500, CYQ11_26550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G1XAZ9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.18 M ammonium citrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→40.72 Å / Num. obs: 117382 / % possible obs: 91.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 39.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rrim(I) all: 0.063 / Χ2: 0.89 / Net I/σ(I): 10.6 / Num. measured all: 208361
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 94.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.445 / Num. measured all: 10979 / Num. unique obs: 6011 / CC1/2: 0.64 / Rpim(I) all: 0.445 / Rrim(I) all: 0.63 / Χ2: 0.77 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.62 Å / SU ML: 0.3505 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 32.2268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 6044 5.15 %RANDOM
Rwork0.234 111240 --
obs0.2371 117284 91.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13757 0 71 683 14511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009814127
X-RAY DIFFRACTIONf_angle_d1.558219017
X-RAY DIFFRACTIONf_chiral_restr0.08332019
X-RAY DIFFRACTIONf_plane_restr0.02762487
X-RAY DIFFRACTIONf_dihedral_angle_d16.29145230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.3922230.34043851X-RAY DIFFRACTION94.37
2.12-2.150.33631960.32653835X-RAY DIFFRACTION94.23
2.15-2.180.34481970.31163883X-RAY DIFFRACTION95.08
2.18-2.20.34892040.30373844X-RAY DIFFRACTION94.78
2.2-2.230.34661750.3453734X-RAY DIFFRACTION90.95
2.23-2.260.49081500.42992936X-RAY DIFFRACTION72
2.26-2.290.32732230.30283800X-RAY DIFFRACTION92.89
2.29-2.330.33192080.28583747X-RAY DIFFRACTION93.32
2.33-2.370.32992000.26143929X-RAY DIFFRACTION95.27
2.37-2.40.30542310.27213849X-RAY DIFFRACTION96.05
2.4-2.450.32812120.27023923X-RAY DIFFRACTION95.78
2.45-2.490.33431840.27183738X-RAY DIFFRACTION91.61
2.49-2.540.35582110.25763880X-RAY DIFFRACTION95.03
2.54-2.590.292270.24223834X-RAY DIFFRACTION94.79
2.59-2.650.36182170.25493868X-RAY DIFFRACTION95.18
2.65-2.710.33471750.26763711X-RAY DIFFRACTION90.58
2.71-2.770.30412130.25393783X-RAY DIFFRACTION94.13
2.77-2.850.32432090.2473822X-RAY DIFFRACTION93.27
2.85-2.930.32162020.24363754X-RAY DIFFRACTION92.6
2.93-3.030.3312140.23593774X-RAY DIFFRACTION92.36
3.03-3.140.32751880.26623708X-RAY DIFFRACTION90.9
3.14-3.260.33921940.25243671X-RAY DIFFRACTION90.18
3.26-3.410.31721850.23033575X-RAY DIFFRACTION86.96
3.41-3.590.28921960.21963360X-RAY DIFFRACTION82.87
3.59-3.810.2591690.21173410X-RAY DIFFRACTION83.88
3.81-4.110.26732040.20523427X-RAY DIFFRACTION84.52
4.11-4.520.25942010.19443595X-RAY DIFFRACTION88.18
4.52-5.170.20621990.19053640X-RAY DIFFRACTION89.89
5.17-6.50.31532060.20923645X-RAY DIFFRACTION89.81
6.5-28.620.23732310.20043714X-RAY DIFFRACTION91.72
Refinement TLS params.Method: refined / Origin x: 13.7601736274 Å / Origin y: 35.7896910664 Å / Origin z: -39.0857512558 Å
111213212223313233
T0.271467211986 Å2-0.00333185362917 Å2-0.00377009769734 Å2-0.307868908301 Å20.0112332943705 Å2--0.281559062046 Å2
L0.134522508904 °2-0.0196430742953 °2-0.00369516570684 °2-0.288821384676 °20.0577373620508 °2--0.110397852156 °2
S-0.0444803783179 Å °0.000808393877335 Å °0.0118173931319 Å °-0.00300060750622 Å °0.04177962756 Å °0.0252049749084 Å °-0.00169786602418 Å °0.0238251336617 Å °0.00387143187171 Å °
Refinement TLS groupSelection details: all

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